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[Application of reverse transcriptase polymerase chain reaction for surveillance of influenza virus in Beijing].

OBJECTIVE: To establish the RT-PCR method to type the influenza virus. METHODS: After amplifying the virus by cell culture, we carried out RT-PCR by using two pairs typing primers and four pairs subtyping primers to detect the influenza virus. RESULTS: In those 23 samples which had cytopathologic changes, there were 10 positive strains detected by RT-PCR assay including seven A type (six H3N2 subtype and one H1N1 subtype) and three B type. CONCLUSION: This method is rapid, specific and sensitive and possesses great value for practical application in the surveillance of influenza virus.

Humans↗

Diagnosis and monitoring of acute cytomegalovirus infection in peripheral blood of transplant recipients by nested reverse transcriptase polymerase chain reaction (RT-PCR).

The aim of this novel diagnostic approach is to monitor cytomegalovirus (CMV) infection in immunocompromised transplant recipients using early, sensitive, and specific predictors before and during antiviral therapy. The peripheral blood cells of 20 patients after transplantation (9 liver, 7 kidney, 4 simultaneous kidney-pancreas) were studied for an early diagnosis of acute infection. The mRNA and DNA of human CMV immediate-early antigen (IEA) were detected by nested-polymerase chain reaction (PCR) assay. Results of nested PCR were compared with the immunological detection of antigen pp65 and serological diagnosis of CMV infection. All data were correlated with clinical symptoms like leukopenia, thrombopenia, pneumonia, and allograft-rejection reaction. Of 20 transplant recipients, 12 were infected by CMV, and 9 suffered from a CMV-related disease. CMV mRNA were detected simultaneously with antigen pp65 and CMV DNA in all patients with symptomatic infection. Additionally, CMV mRNA was found over a longer period after ganciclovir treatment of infected recipients. Nested reverse transcriptase (RT)-PCR for CMV-IEA mRNA allows a sensitive and specific diagnosis of an acute CMV infection. CMV mRNA was found to be a good marker of acute viremia and could be a useful tool for CMV monitoring over the whole period of disease management, even during antiviral therapy.

Cytomegalovirus↗

Direct in situ reverse transcriptase polymerase chain reaction for detection of measles virus.

New methods are described for combined intracellular reverse transcription (RT) and polymerase chain reaction (PCR) using single primer pairs, with direct incorporation of digoxigenin-11-dUTP into amplificants (direct in situ RT/PCR). Routinely used fixatives and minimal pre-treatments were employed. Target sequences of measles virus nucleocapsid (N) and phosphoprotein genes were detected within measles virus infected Vero cells, both in suspension and in formalin-fixed sections, that had been treated by in situ reverse transcription and 30 cycles of direct in situ PCR. Uninfected cells, omission of Taq polymerase, and irrelevant primers were used as controls. Distribution of measles virus within infected cells was determined by in situ hybridisation and immunocytochemistry for measles virus N gene and protein, respectively. Confirmation of amplification within sections was by gel electrophoresis, Southern blotting and sequencing of extracted amplicons. In the majority of cases, measles-infected cells exhibited intense cytoplasmic signal after direct in situ PCR; this was not seen in uninfected cells or infected cells reacted either with irrelevant primers or without Taq polymerase. Unfixed cells in suspension required nested reaction. Measles-specific in situ hybridisation and immunocytochemistry gave an identical signal distribution in sections. Nuclear artifact occurred in some sections and was unpredictable, although it was greatest either in areas of cellular damage, following DNase predigestion, or with vigorous protease pre-treatment. In situ RT-PCR is feasible for measles virus in acutely infected cells both in sections and in suspension. Further work is required to improve the procedure and to eliminate artefactual nuclear signal.

Animals↗

Demonstration of cytokeratin-5 non-expression in tobacco related oral carcinogenesis--use of reverse transcriptase polymerase chain reaction as a sensitive assay.

Cytokeratins (CK) are the epithelia specific intermediate filament proteins. We have shown consistent non-expression of CK-5 protein in human oral pre-cancer and cancer, in earlier studies. To investigate whether non-expression of CK-5 protein is the result of transcriptional or translational block and to evaluate the possibility if CK-5 non-expression can be used as a marker for early diagnosis of tobacco related oral cancer, RT-PCR using CK-5 specific primers was conducted. Out of 36 precancerous lesions and 29 squamous cell carcinomas (SCC) of buccal mucosa (BM) samples studied, 11 and 13 samples respectively of precancer and SCC did not show CK-5 product in RT-PCR. Down regulation of CK-5 mRNA expression was also observed in some samples. Thus, in conclusion, our results have shown that CK-5 non-expression is the result of transcriptional block. We proposed CK-5 non-expression as a potential marker for the early diagnosis of tobacco related oral cancer.

Carcinoma, Squamous Cell↗

Association of drowning and myocarditis in a pediatric population: an autopsy-based study.

CONTEXT: Drowning is a frequent cause of accidental death in childhood, but the association of myocarditis and drowning has only rarely been reported. OBJECTIVE: To report 5 cases of drowning in children with coexistent myocarditis. DESIGN: A retrospective review of autopsy records of patients 0 years to 18 years of age was performed during a 6-year period (1998-2003, total cases reviewed = 1431). RESULTS: Twenty-two drownings were identified, in 14 male and 8 female children. Five patients (23%), 3 female and 2 male children, had coexistent myocarditis. The 5 patients ranged in age from 23 months to 13 years (mean, 7 years 2 months). None of the patients had antecedent symptomatology suggestive of myocarditis. In all patients, the myocarditis was focal mild or moderate, and the inflammatory infiltrate comprised lymphocytes with smaller numbers of neutrophils. All 5 patients had foci of myocyte necrosis. One patient had histologic evidence of myocardial hypertrophy but no evidence of a cardiomyopathy. Microbiologic studies, including culture, immunohistochemistry, polymerase chain reaction, and reverse transcriptase polymerase chain reaction, revealed Mycoplasma pneumoniae DNA in 1 case. CONCLUSIONS: The finding of myocarditis in a significant proportion of drowning victims in this series highlights the importance of a thorough autopsy examination in apparently straightforward cases and has clinicopathologic significance.

Adolescent↗

Detection and molecular characterization of porcine enteric calicivirus in Korea, genetically related to sapoviruses.

Porcine enteric calicivirus (PECV) shares morphological and genetical similarities with Sapoviruses (SVs), which are the leading cause of epidemic, non-bacterial gastroenteritis in children worldwide. The aim of this study was to identify the prevalence of PECV infection in pig farms in Korea, and to compare the evolutionary inter-relationships between Korean PECVs and other caliciviruses. Among 102 diarrhoeic faecal samples of sucking (n = 50) and weaned (n = 52) piglets from 31 different farms in Korea, five samples (4.9%) were detected positive by reverse-transcriptase polymerase chain reaction (PCR), but nine (8.8%) by nested-PCR. Furthermore, we found that Korean PECVs are closely related to SVs.

Animals↗

Laser capture microdissection and real-time reverse transcriptase/ polymerase chain reaction of bronchiolar epithelium after bleomycin.

Terminal airways are affected in many lung diseases and toxic inhalations. To elucidate the changes in terminal airways in these diverse situations it will be helpful to profile and quantify gene expression in terminal bronchiolar epithelium. We used laser capture microdissection (LCM) to collect terminal bronchiolar epithelial cells from frozen sections of lungs of mice subjected to intratracheal bleomycin. The RNA from these cells was used for analysis of select messenger RNAs (mRNAs) by quantitative real-time polymerase chain reaction (PCR). In parallel, we used real-time PCR to analyze mRNAs in whole-lung homogenates prepared from other mice given intratracheal bleomycin. We found reductions of Clara cell-specific protein and keratinocyte growth factor receptor mRNAs in both terminal bronchiolar epithelium and whole-lung homogenates 7 d after bleomycin. In contrast, terminal bronchiolar epithelial transforming growth factor (TGF)-alpha mRNA was reduced but whole-lung TGF-alpha mRNA was not changed, whereas terminal bronchiolar epithelial epidermal growth factor (EGF) receptor mRNA was not changed but whole-lung EGF receptor was reduced. We conclude that LCM can isolate terminal bronchiolar epithelial cells for studies of cell-specific gene expression by quantitative real-time PCR, and that cell-specific gene expression in terminal bronchiolar epithelium is not necessarily reflected in analysis of whole-lung gene expression.

Animals↗

Reverse transcriptase polymerase chain reaction (RT-PCR) detection of HLP gene expression in Candida glabrata and its possible role in in vitro haemolysin production.

Although haemolysins are known to be putative virulence factors contributing to pathogenicity in Candida species, the haemolytic activity of Candida glabrata and its genetic expression is ill understood at present. Thus, we studied a total of 34 Candida glabrata isolates for their in vitro haemolytic activity using a previously described plate assay system. The mRNA expression of HLP, a putative haemolysin gene, of these isolates was also evaluated using a semi-quantitative, non-competitive RT-PCR assay. All 34 C. glabrata isolates exhibited both partial (alpha) and complete (beta) haemolytic activity to varying degrees. In parallel with the haemolytic activity, all isolates were also positive for HLP mRNA expression. The expression levels of HLP mRNA (as relative units) ranged from 1.01 to 1.82, with a mean value of 1.32. On regression analysis of latter values and the haemolytic activity (in terms of the dimension of the haemolytic zone in the plate assay) of the C. glabrata isolates a highly significant positive correlation was noted (r=0.759, p<0.0001). Taken together, our data illustrate not only the phenotypic characteristics of haemolysin(s) and HLP expression of a battery of C. glabrata clinical isolates, but also, for the first time, evidence for a role of HLP in haemolysis.

Base Sequence↗

Cytogenetics, fluorescence in situ hybridization, and reverse transcriptase polymerase chain reaction are necessary to clarify the various mechanisms leading to an MLL-AF10 fusion in acute myelocytic leukemia with 10;11 rearrangement.

In acute myelocytic leukemia (AML), predominantly in AML M5a, a recurrent chromosome aberration involves 11q23/MLL and the short arm of chromosome 10. Molecular studies have shown that the AF10 gene at 10p12 is consistently a partner gene in cases with 10;11 rearrangement. A simple reciprocal translocation cannot lead to the known MLL-AF10 fusion transcript because the 3' part of the MLL gene is orientated to the telomere and the 3' part of the AF10 gene to the centromere. In a series of 1897 AML samples, 14 cases (0.74%) showed 10;11 rearrangements leading to a MLL-AF10 fusion transcript. These cases were analyzed in detail with G banding analyses, fluorescence in situ hybridization, and molecular investigation in a single center. Five different mechanisms of (10;11) rearrangements leading to a MLL-AF10 fusion transcript can be observed (i.e., reciprocal translocations, insertions of either 10p into 11q or 11q into 10p, as well as complex and cryptic rearrangements). Compared to translocations involving MLL and other partner genes, complex rearrangements are unique for MLL-AF10 fusions. This may result from the opposite orientation of MLL and AF10.

Adult↗

[Detection of malignancy markers in thyroid nodules by reverse transcriptase polymerase chain reaction (RT-PCR)].

BACKGROUND: Nodular thyroid disease is a very common disorder with a low frequency of malignancy. The most accurate diagnostic test is fine needle aspiration biopsy (FNAB) of nodules with cytological analysis of the sample. However, this procedure has some limitations in the diagnosis of follicular and papillary thyroid carcinoma. AIM: To detect mRNA from specific malignancy markers in thyroid nodules and to evaluate their potential correlation with cytological and pathological diagnosis. PATIENTS AND METHODS: In 20 patients with thyroid nodules FNAB was performed prior to surgery. The main part of the FNAB sample was used to perform classical cytology. In the remaining of the sample were detected MUC-1, CD26, galectin-3 and TSH receptor mRNAs by RT-PCR technique. RESULTS: Eight patients had positive cytology for papillary cancer, which was confirmed by pathology. Nine had suspicious or non conclusive cytological findings and 3 were negative for neoplastic cells; all 12 were pathologically benign. We detected TSH receptor and galectin-3 mRNA in almost all benign and malignant nodules. MUC-1 was present in 5/8 papillary carcinoma (62.5%), and 1/12 benign nodules (8.3%). CD26 was detected in 7/8 papillary carcinomas but also in 8/12 benign nodules. CONCLUSIONS: RT-PCR can be performed in very small samples of thyroid tissue to detect several mRNA markers. MUC-1 can be a potentially useful marker of malignancy in thyroid nodules. It can be detected by RT-PCR as a complementary technique in the diagnostic evaluation of thyroid nodules.

Biomarkers, Tumor↗

Comparison of detection techniques for cytokine reverse transcriptase polymerase chain reaction; digoxigenin-labeled polymerase chain reaction permits sensitive detection of cytokine mRNA in rat heart allografts.

The polymerase chain reaction (PCR) is a sensitive method for the analysis of cytokine mRNA expression. The amount of specific mRNA in tissues involved in an inflammatory immune response can be low and therefore requires highly sensitive detection of the PCR products. In our study we have compared different detection techniques in order to replace the commonly used detection by means of radiolabeled probes. Besides the detection of DNA in agarose gels by ethidium bromide (EB), we used detection by digoxigenin (DIG)-labeled probes, as well as the direct incorporation of DIG-labeled nucleotides in the PCR, in comparison to detection by means of 32P-labeled probes. In vitro activated rat lymph node cells, lymph node tissue, and acutely or chronically rejected rat heart allografts were examined for expression of mRNA of the cytokines IL-2 and IFNgamma. The directly DIG-labeled PCR appeared to be the best alternative for detection of PCR products by means of radiolabeled probes. While IL-2 mRNA was not detected by means of EB and IFNgamma mRNA was only detected at the highest PCR cycle numbers in acutely and chronically rejected rat heart allografts, both cytokine mRNA's were readily detected by directly DIG-labeled PCR.

Animals↗

Molecular identification of the liver- and the heart-type fatty acid-binding proteins in human and rat kidney. Use of the reverse transcriptase polymerase chain reaction.

The cDNAs of two types of fatty acid-binding protein (FABP) present in human kidney, previously described as types A and B, were isolated using reverse transcriptase-PCR (RT-PCR) with human kidney mRNA and various sets of primers. The cDNA fragments were cloned and sequenced. Renal FABP type A and B cDNAs appeared to be completely identical to human liver- and heart-type FABP cDNAs respectively. In the second part of this study we demonstrated the presence of liver-type FABP in rat kidney by chromatography, e.l.i.s.a. and immunocytochemistry. The ratio and cellular distribution of the two FABP types varies markedly in human and rat kidney. Using RT-PCR we were also able to prepare and identify liver- and heart-type FABP cDNAs with mRNA from both male and female rat kidney.

Animals↗

Detection of human metapneumovirus in respiratory secretions by reverse-transcriptase polymerase chain reaction, indirect immunofluorescence, and virus isolation in human bronchial epithelial cells.

Over two winters in Newcastle upon Tyne, respiratory secretions, negative by immunofluorescence staining for other respiratory viruses, were tested for the presence of human metapneumovirus (HMPV) by RT-PCR. In the second winter, specimens were also tested by immunofluorescence staining with an anti-HMPV polyclonal rabbit antiserum and immunofluorescence positive specimens were inoculated into a line of human bronchiolar cells, 16HBE140. Overall, 55 of 549 (10%) specimens tested were positive for HMPV by RT-PCR. Of 162 specimens tested by both RT/PCR and immunofluorescence staining, 23 were positive by both techniques. Of five specimens positive by RT-PCR alone, only one was confirmed with a second set of primers. Of three specimens positive by immunofluorescence alone, only one was confirmed by virus culture. All four previously recognized sub-genotypes of the virus were identified by both RT-PCR and immunofluorescence staining. Sub-genotype A1 was prevalent in the first winter and B1 prevalent in the second. HMPV replication and virus isolation rates were higher in 16HBE140 cells than in monkey kidney cells and did not require exogenous trypsin. Low passage isolates of both sub-genotypes A2 and B1 replicated slowly reaching peak titers only 12 days after inoculation. In summary, single round RT/PCR and immunofluorescence staining with a polyclonal rabbit antiserum proved of equal sensitivity in the diagnosis of HMPV infection in respiratory secretions both detecting 96% of confirmed positive specimens. 16HBE40 cells provided a significant improvement on monkey kidney cells for the isolation and propagation of the virus.

Animals↗

Evaluation of candidate control genes for diagnosis and residual disease detection in leukemic patients using 'real-time' quantitative reverse-transcriptase polymerase chain reaction (RQ-PCR) - a Europe against cancer program.

Real-time quantitative RT-PCR (RQ-PCR) is a sensitive tool to monitor minimal residual disease (MRD) in leukemic patients through the amplification of a fusion gene (FG) transcript. In order to correct variations in RNA quality and quantity and to calculate the sensitivity of each measurement, a control gene (CG) transcript should be amplified in parallel to the FG transcript. To identify suitable CGs, a study group within the Europe Against Cancer (EAC) program initially focused on 14 potential CGs using a standardized RQ-PCR protocol. Based on the absence of pseudogenes and the level and stability of the CG expression, three genes were finally selected: Abelson (ABL), beta-2-microglobulin (B2M), and beta-glucuronidase (GUS). A multicenter prospective study on normal (n=126) and diagnostic leukemic (n=184) samples processed the same day has established reference values for the CG expression. A multicenter retrospective study on over 250 acute and chronic leukemia samples obtained at diagnosis and with an identified FG transcript confirmed that the three CGs had a stable expression in the different types of samples. However, only ABL gene transcript expression did not differ significantly between normal and leukemic samples at diagnosis. We therefore propose to use the ABL gene as CG for RQ-PCR-based diagnosis and MRD detection in leukemic patients. Overall, these data are not only eligible for quantification of fusion gene transcripts, but also for the quantification of aberrantly expressed genes.

Archives↗

Reverse transcriptase polymerase chain reaction as a reliable method to detect epidermal growth factor receptor exon 2-7 gene deletion in human glioblastomas.

Epidermal growth factor receptor (EGFR) gene amplification has been reported to occur in diverse carcinoma types such as lung, ovarian, and breast carcinomas and in glioblastomas. A 801-bp in-frame deletion close to the aminoterminus of the receptor protein has been found to occur more or less frequently within at least three of these tumor entities. We studied EGFR gene alterations using the polymerase chain reaction and EGFR gene expression of 65 astrocytic tumors (51 glioblastomas World Health Organization [WHO] IV, five anaplastic astrocytomas WHO III, and nine astrocytomas WHO II). EGFR gene amplification, as determined by Southern blotting using a full-length cDNA probe, was observed in 22 of 51 glioblastomas (43%) but in none of the grade II astrocytomas. Two of five anaplastic astrocytomas at WHO III showed a considerable degree of EGFR amplification but, according to the neuroradiological data, these two tumors had to be considered as glioblastomas. The most frequently found genetic alteration was the 801-bp deletion near the receptor aminoterminus comprising a complete loss of exon 2 to exon 7 (del2-7). We showed that RT-PCR is superior to Southern blot analysis in detection of this type of deletion and can be assigned to 9 of 38 (24%) glioblastomas examined. Expression of a EGF receptor protein was enhanced in most of the tumors with gene amplification. However, 5 of 18 tumors that express a receptor protein in the absence of EGFR gene amplification also showed elevated levels of EGFR gene expression. In addition to the full-length receptor protein, a signal in the 140-kDa range was observed in 17 of 35 glioblastomas (49%). This fragment may correspond to the truncated de12-7 receptor protein or might be due to proteolysis of the full-length receptor protein.

Blotting, Southern↗

Repetitive and site-specific molecular staging of prostate cancer using nested reverse transcriptase polymerase chain reaction for prostate specific antigen and prostate specific membrane antigen.

We performed repetitive molecular staging using, nested rt-PCR for PSA and PSM at the peripheral blood (PB) and bone marrow (BM) of patients with prostate cancer (Pr.Ca) and benign prostate hyperplasia (BPH) after transrectal ultrasonography-guided biopsy (TRUS-B; 6-9 biopsies/patient), Pr.Ca patients after radical prostatectomy (RP), and Pr.Ca patients with diffuse bony metastases. All BPH patients (N = 20) tested negative at BM. Of the 2 who tested positive at PB 2 weeks after TRUS-B tested negative 8 weeks after TRUS-B. Of the 17 Pr.Ca, 7 (41.2%) tested positive at PB for PSA and PSM 2 weeks after TRUS-B while only 4 (23.5%) of them tested positive at repetitive analysis 8 weeks after TRUS-B. Two (11.8%) of the 17 Pr.Ca patients had positive analysis at BM for PSA and PSM 2 and 8 weeks after TRUS-B. Of 12 Pr.Ca patients with negative pre-operative molecular staging, 7 (58.3%) tested positive at PB for PSA and PSM 2 months post-RP but only 3 (25%) of them re-tested positive 12 months post-RP. Of these 12 Pr.Ca, 4 (33.3%) tested positive at BM for PSA and PSM 2 months post-RP while none re-tested positive 12 months post-RP. All Pr.Ca (N = 20) with diffuse bony lesions tested positive at BM. At PB, 6 of them (30%) tested negative for both PSA and PSM. Our data suggest that nested rt-PCR for PSA and PSM at PB is affected by TRUS-B and RP, while such analysis at BM concerted diffuse bony disease.

Adult↗

Combining in situ reverse transcriptase polymerase chain reaction, optical microscopy, and X-ray photoelectron spectroscopy to investigate mineral surface-associated microbial activities.

A study was undertaken to investigate expression of a gene encoding a c-type cytochrome in cells of the dissimilatory metal reducing bacterium (DMRB) Geobacter sulfurreducens during association with poorly crystalline and crystalline solid-phase Fe(III)-oxides. The gene encoding OmcC (outer membrane c-type cytochrome) was used as a target for PCR-based molecular detection and visualization of omcC gene expression by individual cells and aggregates of cells of G. sulfurreducens associated with ferrihydrite and hematite mineral particles. Expression of omcC was demonstrated in individual bacterial cells associated with these Fe-oxide surfaces by in situ RT-PCR (IS-RT PCR) and epifluorescence microscopy. Epifluorescence microscopy also permitted visualization of total DAPI-stained cells in the same field of view to assess the fraction of the cell population expressing omcC. By combining reflected differential interference contrast (DIC) microscopy and epifluorescence microscopy, it was possible to determine the spatial relationship between cells expressing omcC and the mineral surface. Introduction of the fluorescently labeled lectin concanavalin A revealed extracellular polymeric substances (EPS) extending between aggregations of bacterial cells and the mineral surface. The results indicate that EPS mediates an association between cells of G. sulfurreducens and ferrihydrite particles, but that direct cell contact with the mineral surface is not required for expression of omcC. XPS analysis revealed forms of reduced Fe associated with areas of the mineral surface where EPS-mediated bacterial associations occurred. The results demonstrate that by combining molecular biology, reflectance microscopy, and XPS, chemical transformations at a mineral surface can be related to the expression of specific genes by individual bacterial cells and cell aggregates associated with the mineral surface. The approach should be useful in establishing involvement of specific gene products in a wide variety of surface chemical processes.

Bacterial Proteins↗

Standardization and quality control studies of 'real-time' quantitative reverse transcriptase polymerase chain reaction of fusion gene transcripts for residual disease detection in leukemia - a Europe Against Cancer program.

Detection of minimal residual disease (MRD) has proven to provide independent prognostic information for treatment stratification in several types of leukemias such as childhood acute lymphoblastic leukemia (ALL), chronic myeloid leukemia (CML) and acute promyelocytic leukemia. This report focuses on the accurate quantitative measurement of fusion gene (FG) transcripts as can be applied in 35-45% of ALL and acute myeloid leukemia, and in more than 90% of CML. A total of 26 European university laboratories from 10 countries have collaborated to establish a standardized protocol for TaqMan-based real-time quantitative PCR (RQ-PCR) analysis of the main leukemia-associated FGs within the Europe Against Cancer (EAC) program. Four phases were scheduled: (1) training, (2) optimization, (3) sensitivity testing and (4) patient sample testing. During our program, three quality control rounds on a large series of coded RNA samples were performed including a balanced randomized assay, which enabled final validation of the EAC primer and probe sets. The expression level of the nine major FG transcripts in a large series of stored diagnostic leukemia samples (n=278) was evaluated. After normalization, no statistically significant difference in expression level was observed between bone marrow and peripheral blood on paired samples at diagnosis. However, RQ-PCR revealed marked differences in FG expression between transcripts in leukemic samples at diagnosis that could account for differential assay sensitivity. The development of standardized protocols for RQ-PCR analysis of FG transcripts provides a milestone for molecular determination of MRD levels. This is likely to prove invaluable to the management of patients entered into multicenter therapeutic trials.

Biomarkers, Tumor↗